Oh, hey. Thanks for asking, I've been wondering this too!
I'm not sure I agree with this, though:
"Top Skills" count 3 times more (for Skyrim characters).
Like a few other things that have come up, it's a difference between the way the site programmers intended the site to work and the way in which people are using it. Perhaps you intended for people to set the Top Skills to be the
highest level skills which their characters have attained? But that's not how I use the site. My characters' "Top Skills" are the skills which are most important for my character in a
roleplaying sense, since they are the skills which are displayed on their signature file card.
For example, my character who is based on Martin Septim has Destruction, One-handed, and Speech as his Top Skills - since the primary skills that Martin uses in Oblivion are Destruction magic (Ice) and one-handed Blade weapons, and he is very charming and persuasive. These are by no means his highest level skills - he has only reached level 88 in Destruction and level 93 in One-handed. I do not like the idea that players could manipulate their scores by simply choosing different Top Skills

.
If you are able to access the data easily (e.g. if you have a beta version of the site), it might be interesting to recalculate every Skyrim character's score by taking the three highest stats. Or, perhaps (if it's easier) to recalculate the scores with the Top Skills being worth the same as others.